tbuckley/cabot-search huggingface dataset:
Evaluation of the Global Lung Function Initiative 2012 reference values for spirometry in China: a national cross-sectional study
Authors: Feilong Wang, Kun Wang, Cole Bowerman, Hogne Ulla, Jiaxing Sun, Marko Topalovic, Sanja Stanojevic, Qiang Li
Journal: European Respiratory Journal (2022)

<b>GLI South East Asian equations fit well across a contemporary North and South Chinese population. This study suggests a single reference equation for spirometry can be applied to the Chinese population.</b>https://bit.ly/3zhCc2w
Functional inference of gene regulation using single-cell multi-omics
Authors: Vinay K. Kartha, Fabiana M. Duarte, Yan Hu, Sai Ma, Jennifer G. Chew, Caleb A. Lareau, Andrew Earl, Zach D. Burkett, Andrew S. Kohlway, Ronald Lebofsky, Jason D. Buenrostro
Journal: Cell Genomics (2022)
Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics
Authors: Daniel Podlesny, Marija Durdevic, Sudarshan Paramsothy, Nadeem O. Kaakoush, Christoph Högenauer, Gregor Gorkiewicz, Jens Walter, W. Florian Fricke
Journal: Cell Reports Medicine (2022)

Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-associated pathologies, but our understanding of the post-FMT microbiome assembly process and its ecological and clinical determinants is incomplete. Here we perform a comprehensive fecal metagenome analysis of 14 FMT trials, involving five pathologies and >250 individuals, and determine the origins of strains in patients after FMT. Independently of the underlying clinical condition, conspecific coexistence of donor and recipient strains after FMT is uncommon and donor strain engraftment is strongly positively correlated with pre-FMT recipient microbiota dysbiosis. Donor strain engraftment was enhanced through antibiotic pretreatment and bowel lavage and dependent on donor and recipient ɑ-diversity; strains from relatively abundant species were more likely and from predicted oral, oxygen-tolerant, and gram-positive species less likely to engraft. We introduce a general mechanistic framework for post-FMT microbiome assembly in alignment with ecological theory, which can guide development of optimized, more targeted, and personalized FMT therapies.
Sensitisation to recombinant<i>Aspergillus fumigatus</i>allergens and clinical outcomes in COPD
Authors: Pei Yee Tiew, Jayanth Kumar Narayana, Marilynn Swee Li Quek, Yan Ying Ang, Fanny Wai San Ko, Mau Ern Poh, Tavleen Kaur Jaggi, Huiying Xu, Kai Xian Thng, Mariko Siyue Koh, Augustine Tee, David Shu Cheong Hui, John Arputhan Abisheganaden, Krasimira Tsaneva-Atanasova, Fook Tim Chew, Sanjay H. Chotirmall
Journal: European Respiratory Journal (2022)

Variable clinical outcomes are reported with fungal sensitisation in chronic obstructive pulmonary disease (COPD), and it remains unclear which fungi and what allergens associate with the poorest outcomes. The use of recombinant as opposed to crude allergens for such assessment is unknown.
The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation
Authors: Anna Yeaton, Geraldine Cayanan, Sanam Loghavi, Igor Dolgalev, Emmett M. Leddin, Christian E. Loo, Hedieh Torabifard, Deedra Nicolet, Jingjing Wang, Kate Corrigan, Varvara Paraskevopoulou, Daniel T Starczynowski, Eric Wang, Omar Abdel-Wahab, Aaron D Viny, Richard M. Stone, John C. Byrd, Olga A. Guryanova, Rahul M. Kohli, G. Andrés Cisneros, Aristotelis Tsirigos, Ann-Kathrin Eisfeld, Iannis Aifantis, Maria Guillamot
Journal: Cancer Discovery (2022)

Abstract Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of mutated preleukemic cells. Individuals with CH are at an increased risk of developing hematopoietic malignancies. Here, we describe a novel animal model carrying a recurrent TET2 missense mutation frequently found in patients with CH and leukemia. In a fashion similar to CH, animals show signs of disease late in life when they develop a wide range of myeloid neoplasms, including acute myeloid leukemia (AML). Using single-cell transcriptomic profiling of the bone marrow, we show that disease progression in aged animals correlates with an enhanced inflammatory response and the emergence of an aberrant inflammatory monocytic cell population. The gene signature characteristic of this inflammatory population is associated with poor prognosis in patients with AML. Our study illustrates an example of collaboration between a genetic lesion found in CH and inflammation, leading to transformation and the establishment of blood neoplasms. Significance: Progression from a preleukemic state to transformation, in the presence of TET2 mutations, is coupled with the emergence of inflammation and a novel population of inflammatory monocytes. Genes characteristic of this inflammatory population are associated with the worst prognosis in patients with AML. These studies connect inflammation to progression to leukemia. See related commentary by Pietras and DeGregori, p. 2234 . This article is highlighted in the In This Issue feature, p. 2221
Impact of air pollution and meteorological factors on incidence of allergic rhinitis: A low‐latitude multi‐city study in China
Authors: Xin Luo, Haiyu Hong, Yongtian Lu, Shumin Deng, Naigeng Wu, Qilin Zhou, Zhuanggui Chen, Peiying Feng, Yuqi Zhou, Jin Tao, Min Dai, Kun Zhang, Pingping Zhang, Yating Li, Guowei Xiong, Yun Cheng, Jing Su, Tingyuan Li, Jingyang Chen, Manhou Chao, Guixian Liang, Qingwu Wu, Min Zhou, Rui Zheng, Shuo Wu, Yana Zhang, Xuekun Huang, Lin Yin, Zifeng Liu, Huanping Lu, Qintai Yang
Journal: Allergy (2022)

Appendix S1 Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Venetoclax ex vivo functional profiling predicts improved progression-free survival
Authors: Vikas A. Gupta, Shannon M. Matulis, Benjamin G. Barwick, R. Devin Bog, Conrad W. Shebelut, Mala Shanmugam, Paola Neri, Nizar J. Bahlis, Madhav V. Dhodapkar, Leonard T. Heffner, Craig C. Hofmeister, Nisha S. Joseph, Sagar Lonial, Jonathan L. Kaufman, David L. Jaye, Ajay K. Nooka, Lawrence H. Boise
Journal: Blood Cancer Journal (2022)
Quantitative approaches in multimodal fundus imaging: State of the art and future perspectives
Authors: Alessandro Arrigo, Emanuela Aragona, Maurizio Battaglia Parodi, Francesco Bandello
Journal: Progress in Retinal and Eye Research (2022)

When it first appeared, multimodal fundus imaging revolutionized the diagnostic workup and provided extremely useful new insights into the pathogenesis of fundus diseases. The recent addition of quantitative approaches has further expanded the amount of information that can be obtained. In spite of the growing interest in advanced quantitative metrics, the scientific community has not reached a stable consensus on repeatable, standardized quantitative techniques to process and analyze the images. Furthermore, imaging artifacts may considerably affect the processing and interpretation of quantitative data, potentially affecting their reliability. The aim of this survey is to provide a comprehensive summary of the main multimodal imaging techniques, covering their limitations as well as their strengths. We also offer a thorough analysis of current quantitative imaging metrics, looking into their technical features, limitations, and interpretation. In addition, we describe the main imaging artifacts and their potential impact on imaging quality and reliability. The prospect of increasing reliance on artificial intelligence-based analyses suggests there is a need to develop more sophisticated quantitative metrics and to improve imaging technologies, incorporating clear, standardized, post-processing procedures. These measures are becoming urgent if these analyses are to cross the threshold from a research context to real-life clinical practice.
Sinus augmentation procedure via the lateral window technique—Reducing invasiveness and preventing complications: A narrative review
Authors: Pascal Valentini, Zvi Artzi
Journal: Periodontology 2000 (2022)

Abstract Sinus augmentation has become an integrated surgical phase in posterior maxillary implant prosthesis reconstruction. Since the residual alveolar bony height usually requires additional volume particularly at this anatomical region, sinus floor augmentation is advocated routinely. Over the years, Implant success rate is proved to be comparable to the one in the pristine bone, which is well documented in the literature. Anatomical aspects as well as surgeon skills are at most importance to achieve predictable outcome. In this narrative review, the different osteotomy techniques, the indications toward 1 or 2‐stage approaches, the control of the Schneiderian membrane integrity as well as the management of intra‐ and post‐operative complications are thoroughly discussed according the current data. In light of the excellent long‐term implant success rate concurrent with the application of contemporary advanced techniques of the sinus augmentation via the lateral wall osteotomy approach, reduce invasiveness and less complication occurrences are well documented. A well‐codified patient selection involving the rhinologist as an integral medical team would be significantly beneficial toward early diagnosis. In‐depth knowledge of the anatomy, execution of a well standardized surgical technique, and understanding the complication etiology and their management are prerequisites for reducing patient morbidity to minimal discomfort and predictable successful outcome.
Can computer‐assisted implant surgery improve clinical outcomes and reduce the frequency and intensity of complications in implant dentistry? A critical review
Authors: Atiphan Pimkhaokham, Sirimanas Jiaranuchart, Boosana Kaboosaya, Sirida Arunjaroensuk, Keskanya Subbalekha, Nikos Mattheos
Journal: Periodontology 2000 (2022)

Abstract Computer‐assisted implant surgery (CAIS), either static or dynamic, is well documented to significantly improve the accuracy of implant placement. Whether the increased accuracy leads to a corresponding improvement in clinical outcomes has not yet been systematically investigated. The aim of this critical review was to investigate whether the use of CAIS can lead to reduction of complications as well as improved clinical and patient‐reported outcomes (PROs) when compared with conventional freehand implant surgery. A comprehensive online search was conducted to identify studies where implants were installed with static computer‐assisted implant surgery (s‐CAIS)or dynamic computer‐assisted implant surgery(d‐CAIS) or combinations of the two, either compared with conventional free‐hand implant placement or not. Seventy‐seven studies were finally included in qualitative analysis, while data from three studies assessing postsurgical pain were suitable for a meta‐analysis. Only a small number of the available studies were comparative. The current evidence does not suggest any difference with regard to intraoperative complications, immediate postsurgical healing, osseointegration success, and survival of implants placed with CAIS or freehand protocols. Intraoperative and early healing events as reported by patients in randomized clinical trials (RCTs) did not differ significantly between CAIS used with flap elevation and conventional implant placement. There is limited evidence that increased accuracy of placement with CAIS is correlated with superior esthetic outcomes. Use of CAIS does not significantly reduce the length of surgeries in cases of single implants and partially edentulous patients, although there appears to be a more favorable impact in fully edentulous patients. Although CAIS alone does not seem to improve healing and the clinical and PRO, to the extent that it can increase the utilization of flapless surgery and predictability of immediacy protocols, its use may indirectly lead to substantial improvements in all of the above parameters.
Clinical and virological characteristics of SARS-CoV-2 Omicron BA.2.2 variant outbreaks during April to May, 2022, Shanghai, China
Authors: Yuanyun Ao, Jingjing Li, Zhongqiu Wei, Zhonglin Wang, He Tian, Yue Qiu, Xiaomin Fu, Wenjie Ma, Liting Li, Mei Zeng, Jin Xu
Journal: Journal of Infection (2022)
Anti-inflammatory clearance of amyloid-β by a chimeric Gas6 fusion protein
Authors: Hyuncheol Jung, Se Young Lee, Seongjoon Lim, Hyeong Ryeol Choi, Yeseong Choi, Minjin Kim, Segi Kim, Yujean Lee, Kyung Ho Han, Won-Suk Chung, Chan Hyuk Kim
Journal: Nature Medicine (2022)
Determining and reporting minimal important change for patient-reported outcome instruments in pulmonary medicine
Authors: Jeff Swigris, Brandon Foster, Nathan Johnson
Journal: European Respiratory Journal (2022)

<b>Utilising consistent terminology and a rigorous approach to determining and reporting minimal important change to the patient (MICP) would elevate quality of measurement science in our field and bolster confidence in using PROs as first-tier endpoints</b>https://bit.ly/3OOGNhc
Relieving DYRK1A repression of MKL1 confers an adult-like phenotype to human infantile megakaryocytes
Authors: Kamaleldin E. Elagib, Ashton Brock, Cara M. Clementelli, Goar Mosoyan, Lorrie L. Delehanty, Ranjit K. Sahu, Alexandra Pacheco-Benichou, Corinne Fruit, Thierry Besson, Stephan W. Morris, Koji Eto, Chintan Jobaliya, Deborah L. French, Paul Gadue, Sandeep Singh, Xinrui Shi, Fujun Qin, Robert Cornelison, Hui Li, Camelia Iancu-Rubin, Adam N. Goldfarb
Journal: Journal of Clinical Investigation (2022)

Infantile (fetal and neonatal) megakaryocytes (Mks) have a distinct phenotype consisting of hyperproliferation, limited morphogenesis, and low platelet production capacity. These properties contribute to clinical problems that include thrombocytopenia in neonates, delayed platelet engraftment in recipients of cord blood stem cell transplants, and inefficient ex vivo platelet production from pluripotent stem cell-derived Mks. The infantile phenotype results from deficiency of the actin-regulated coactivator, MKL1, which programs cytoskeletal changes driving morphogenesis. As a strategy to complement this molecular defect, we screened pathways with the potential to affect MKL1 function and found that DYRK1A inhibition dramatically enhanced Mk morphogenesis in vitro and in vivo. Dyrk1 inhibitors rescued enlargement, polyploidization, and thrombopoiesis in human neonatal Mks. Mks derived from induced pluripotent stem cells responded in a similar manner. Progenitors undergoing Dyrk1 inhibition demonstrated filamentous actin assembly, MKL1 nuclear translocation, and modulation of MKL1 target genes. Loss-of-function studies confirmed MKL1 involvement in this morphogenetic pathway. Expression of Ablim2, a stabilizer of filamentous actin, increased with Dyrk1 inhibition, and Ablim2 knockdown abrogated the actin, MKL1, and morphogenetic responses to Dyrk1 inhibition. These results delineate a pharmacologically tractable morphogenetic pathway whose manipulation may alleviate clinical problems associated with the limited thrombopoietic capacity of infantile Mks.
Author Correction: Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix
Authors: Emily J. Kay, Karla Paterson, Carla Riera-Domingo, David Sumpton, J. Henry M. Däbritz, Saverio Tardito, Claudia Boldrini, Juan R. Hernandez-Fernaud, Dimitris Athineos, Sandeep Dhayade, Ekaterina Stepanova, Enio Gjerga, Lisa J. Neilson, Sergio Lilla, Ann Hedley, Grigorios Koulouras, Grace McGregor, Craig Jamieson, Radia Marie Johnson, Morag Park, Kristina Kirschner, Crispin Miller, Jurre J. Kamphorst, Fabricio Loayza-Puch, Julio Saez-Rodriguez, Massimiliano Mazzone, Karen Blyth, Michele Zagnoni, Sara Zanivan
Journal: Nature Metabolism (2022)
Correction: Expanding syphilis test uptake using rapid dual self-testing for syphilis and HIV among men who have sex with men in China: A multiarm randomized controlled trial
Authors: Cheng Wang, Jason J. Ong, Peizhen Zhao, Ann Marie Weideman, Weiming Tang, M. Kumi Smith, Michael Marks, Hongyun Fu, Weibin Cheng, Fern Terris-Prestholt, Heping Zheng, Joseph D. Tucker, Bin Yang
Journal: PLoS Medicine (2022)

[This corrects the article DOI: 10.1371/journal.pmed.1003930.].
Oncological outcomes of robotic pancreatectomy in patients with pancreatic cancer who receive adjuvant chemotherapy: A propensity score-matched retrospective cohort study
Authors: Yuanchi Weng, Ziyun Shen, Georgios Gemenetzis, Jiabin Jin, Haoda Chen, Xiaxing Deng, Chenghong Peng, Baiyong Shen
Journal: International Journal of Surgery (2022)

Limited data are available regarding long-term oncological outcomes in patients with pancreatic ductal adenocarcinoma (PDAC) who undergo robotic pancreatectomy (RP).All patients who underwent RP and open pancreatectomy (OP) for resectable PDAC between January 2011 and December 2019 were included. The RP group was matched 1:1 with OP group by propensity score matching (PSM). The oncological outcomes were collected and analyzed.Overall, 1606 patients were included in this study. After PSM, a well-balanced cohort of 335 patients in each group was selected for further analysis. The RP group had shorter operative time (210 min vs. 240 min, P < 0.001), lower estimated blood loss (200 ml vs. 300 ml, P = 0.011), lower wound infection rates (4.5% vs. 10.1%, P = 0.005) and shorter length of postoperative hospital stay (15 days vs. 17 days, P = 0.001) compared to the OP group, with no significant differences in other perioperative outcomes. OS was comparable between the two groups (31 months vs. 28 months, P = 0.077); however, RFS was improved in the RP group (17 months vs. 14 months, P = 0.015). Subgroup analysis showed that patients who received adjuvant chemotherapy (AC) in the RP group had better RFS than the similar patient cohort in the OP group (17 months vs. 14 months, P = 0.024).Robotic pancreatectomy is safe and oncologically effective for resectable PDAC. OS was comparable between RP and OP, and RFS was improved in the RP group, especially in patients who receive AC.
BCL10 Mutants: Architects of Oncogenic Signaling Provide a Blueprint for Precision Medicine
Authors: James D. Phelan, Thomas Oellerich
Journal: Cancer Discovery (2022)

Summary: BCL10, a key activator of NF-κB downstream of oncogenic B-cell receptor signaling, is mutated in nearly 40% of the BN2/C1 genetic subtype of diffuse large B-cell lymphoma, but how these mutations function to augment signaling and their relevance to targeted precision medicine agents remains unclear. In this issue of Cancer Discovery, Xia and colleagues demonstrate distinct mechanisms of oncogenic signaling regulation and therapeutic vulnerabilities among different recurrent BCL10 mutations. See related article by Xia et al., p. 1922 (1).
Belly Fat Weakens Immune Fitness
Authors: Jose R. Conejo-Garcia, Tyler J. Curiel
Journal: Cancer Discovery (2022)

Summary: Much work has been done to reduce cancer immunosuppression through inhibiting soluble proteins, surface molecules, and suppressive cells. This article shows an important role for the lipid lysophosphatidic acid, whose suppression shows promise as a novel cancer immunotherapeutic, demonstrated in ovarian cancer. See related article by Chae et al., 1904 (5).
Hiding in Plain Sight: A Novel Microbial Driver for Colorectal Cancer?
Authors: Tejeshwar Jain, Vikas Dudeja
Journal: Cancer Discovery (2022)

Summary: In this issue of Cancer Discovery, Drewes and colleagues demonstrate a surprising role for the common gut pathogen Clostridioides difficile in driving colorectal cancer in preclinical models through the bacterial toxin–dependent reprogramming of the epithelial and immune compartments. See related article by Drewes et al., p. 1873 (3).
Upscaling human mesenchymal stromal cell production in a novel vertical-wheel bioreactor enhances extracellular vesicle secretion and cargo profile
Authors: Richard Jeske, Chang Liu, Leanne Duke, Maria L. Canonicco Castro, Laureana Muok, Peggy Arthur, Mandip Singh, Sunghoon Jung, Li Sun, Yan Li
Journal: Bioactive Materials (2022)

Human mesenchymal stromal cells (hMSCs) are mechanically sensitive undergoing phenotypic alterations when subjected to shear stress, cell aggregation, and substrate changes encountered in 3D dynamic bioreactor cultures. However, little is known about how bioreactor microenvironment affects the secretion and cargo profiles of hMSC-derived extracellular vesicles (EVs) including the subset, "exosomes", which contain therapeutic proteins, nucleic acids, and lipids from the parent cells. In this study, bone marrow-derived hMSCs were expanded on 3D Synthemax II microcarriers in the PBS mini 0.1L Vertical-Wheel bioreactor system under variable shear stress levels at 25, 40, and 64 RPM (0.1-0.3 dyn/cm2). The bioreactor system promotes EV secretion from hMSCs by 2.5-fold and upregulates the expression of EV biogenesis markers and glycolysis genes compared to the static 2D culture. The microRNA cargo was also altered in the EVs from bioreactor culture including the upregulation of miR-10, 19a, 19b, 21, 132, and 377. EV protein cargo was characterized by proteomics analysis, showing upregulation of metabolic, autophagy and ROS-related proteins comparing with 2D cultured EVs. In addition, the scalability of the Vertical-Wheel bioreactor system was demonstrated in a 0.5L bioreactor, showing similar or better hMSC-EV secretion and cargo content compared to the 0.1L bioreactor. This study advances our understanding of bio-manufacturing of stem cell-derived EVs for applications in cell-free therapy towards treating neurological disorders such as ischemic stroke, Alzheimer's disease, and multiple sclerosis.
Daily tenofovir disoproxil fumarate/emtricitabine and hydroxychloroquine for pre-exposure prophylaxis of COVID-19: a double-blind placebo-controlled randomized trial in healthcare workers
Authors: Rosa Polo, Xabier García-Albéniz, Carolina Terán, Miguel Morales, David Rial-Crestelo, M. Angeles Garcinuño, Miguel García del Toro, César Hita, Juan Luis Gómez-Sirvent, Luis Buzón, Alberto Díaz de Santiago, Jose Pérez Arellano, Jesus Sanz, Pablo Bachiller, Elisa Martínez Alfaro, Vicente Díaz-Brito, Mar Masiá, Alicia Hernández-Torres, Jose M. Guerra, Jesús Santos, Piedad Arazo, Leopoldo Muñoz, Jose Ramon Arribas, Pablo Martínez de Salazar, Santiago Moreno, Miguel A. Hernán, Julia Del Amo, None Julia del Amo, Rosa Polo, Santiago Moreno, Juan Berenguer, Esteban Martínez, Miguel Hernán, Pablo Martínez de Salazar, Xabier García de Albéniz
Journal: Clinical Microbiology and Infection (2022)
When I use a word . . . . Too much healthcare—overdetection
Authors: Jeffrey K Aronson
Journal: BMJ (2022)

I have previously suggested that we should replace the ambiguous term “too much medicine,” in the sense of using too many medical interventions, including diagnostic and therapeutic ones, with the term “too much healthcare.” The first item in my list of the many forms of too much healthcare is too many diagnostic tests (if used inappropriately), or, in a word, overdetection, one of the two major causes of overdiagnosis. Overdetection has been defined as identification of abnormalities that were never going to cause harm, abnormalities that do not progress, that progress too slowly to cause symptoms or harm during a person’s remaining lifetime, or that resolve spontaneously. Large systematic reviews suggest that the problem is rife and increasing. One form of the Ulysses syndrome, repeated tests resulting in more harm than benefit, is a possible consequence of overdetection, especially when false positive tests occur. There are more descriptions of the problem of overdetection than of possible solutions, but education and the use of machine learning algorithms to analyse data have been suggested.